ATLANTA — A federal judge on Monday ordered a delay in the certification of Georgia’s election results, citing concerns about the state’s voter registration system and the handling of provisional ballots. The decision effectively deepened the turmoil in Georgia’s campaign for governor, a still unsettled contest that has been among the most acrimonious campaigns in the nation this year.

Although the ruling by Judge Amy Totenberg of Federal District Court in Atlanta formally affected every election in Georgia for state and federal office, it reverberated most immediately and powerfully through the governor’s race, in which the Democratic candidate, Stacey Abrams, was within 21,000 votes of forcing a runoff election against Brian Kemp, the Republican nominee.

Georgia’s secretary of state, Robyn A. Crittenden, had been preparing to certify the outcome of the election as soon as Wednesday, one day after Georgia’s 159 counties were to complete their tabulations and six days before state law mandated certification. But in a 56-page ruling on Monday night, Judge Totenberg forbade Ms. Crittenden, who assumed office only last week, from certifying the results until at least Friday evening.

Judge Totenberg, who had already raised concerns about Georgia’s system of elections this year, wrote that the state’s announced timetable for a swift certification “appears to suggest the secretary’s foregoing of its responsibility to confirm the accuracy of the results prior to final certification, including the assessment of whether serious provisional balloting count issues have been consistently and properly handled.”

Georgia allows people to cast provisional ballots in three circumstances, including when a person’s name is not listed on the roster of registered voters at a precinct, and critics of the state have argued that security vulnerabilities had left a government computer system prone to manipulation. Some 21,190 provisional ballots were cast in Georgia, state officials said, about 9,000 more than were submitted in 2014, when the Georgia Governor’s Mansion was last at stake. (Democrats have questioned the state’s data.)

The renewed validity of any ballots could narrow the margin in the already close race for governor. Unofficial returns showed Monday night that even as Mr. Kemp held a lead of about 58,000 votes, he could afford to lose only 21,000 or so votes before facing a runoff election against Ms. Abrams. If Ms. Abrams were to net about 19,000 votes, a recount would be required under state law.

Although Democrats, some of whom had feared that the race would be over by midweek, saw Judge Totenberg’s ruling as a crucial lifeline, it was not clear how much her decision would ultimately influence the election results. Mr. Kemp and his allies have spent recent days promoting him as the mathematically indisputable governor-elect — Mr. Kemp resigned as secretary of state last week “to focus on the transition to my gubernatorial administration” — while Ms. Abrams’s campaign has mounted an aggressive effort to set up a runoff.

Lauren Groh-Wargo, Ms. Abrams’s campaign manager, welcomed Monday night’s decision as “good news.” Mr. Kemp’s campaign did not immediately comment, but in a statement on Monday morning, hours before Judge Totenberg’s ruling, a spokesman asserted that Ms. Abrams “lost, and her concession is long overdue.”

“It’s incredibly shameful that liberal lawyers are doubling down on lawsuits desperately trying to create more votes for Stacey Abrams,” the spokesman, Ryan Mahoney, said. “They don’t want to win this election. They are trying to steal it.”

Judge Totenberg did not issue her decision in one of the cases brought in recent days by Ms. Abrams’s campaign or the Democratic Party of Georgia, which raised, among other issues, concerns about requirements to count absentee ballots and the deadline for those ballots. Rather, her order was in connection to litigation filed by Common Cause, a nonpartisan group, which brought its lawsuit on Nov. 5, one day before the election.

It was only on Monday night, though, that the judge intervened with such force.

“Repeated inaccuracies were identified in the voter registration system that caused qualified voters likely to lose their vote or to be channeled at best into the provisional voting process because their registration records did not appear or had been purged from the data system,” Judge Totenberg, an appointee of former President Barack Obama, wrote.

She added that she had concluded that there was “evidence that certain counties and precincts stintingly provided provisional ballots to voters despite the volume of individuals facing registration issues at the polls.”

Although Judge Totenberg described her order as offering “modest relief,” it could have substantial repercussions as the state tries to complete the process of electing its 83rd governor. In addition to postponing the certification of the vote, Judge Totenberg ordered the secretary of state’s office to create a hotline or website so people who had cast provisional ballots could “determine whether their provisional ballots were counted and if not, the reason why.”

She also ordered that elections officials review the eligibility of many people who cast provisional ballots because of registration issues.

“The right to vote is fundamental, and no one should lose that right because of mistakes in the voter registration database,” Myrna Perez, one of the lawyers involved in the case, said in a statement. “The Georgians who voted in this election deserve better than what the state wanted to give them.”